Structure of PDB 1yy5 Chain A Binding Site BS01

Receptor Information
>1yy5 Chain A (length=498) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQ
GRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERG
RVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQF
LTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVV
QRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQ
SVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECC
WSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLERTSVTCWSQPLFFV
NLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDS
EDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPVDMVVA
MSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKLEHHH
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain1yy5 Chain A Residue 803 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1yy5 Crystal Structures of Fms1 and its Complex with Spermine Reveal Substrate Specificity.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I14 G15 G17 I18 A19 L38 E39 A40 R41 G46 R47 G62 A63 S64 W65 H67 V223 T252 V253 G270 L294 W440 A449 Y450 G478 E479 G487 C488 A489 A492
Binding residue
(residue number reindexed from 1)		I9 G10 G12 I13 A14 L33 E34 A35 R36 G41 R42 G57 A58 S59 W60 H62 V218 T247 V248 G265 L289 W429 A438 Y439 G463 E464 G472 C473 A474 A477
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H67
Catalytic site (residue number reindexed from 1) H62
Enzyme Commision number 1.5.3.17: non-specific polyamine oxidase.
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0016491 oxidoreductase activity
GO:0046592 polyamine oxidase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0052897 N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity
GO:0052901 spermine oxidase activity
GO:0052903 N(1)-acetylpolyamine oxidase (3-acetamidopropanal-forming) activity
Biological Process
GO:0006338 chromatin remodeling
GO:0015940 pantothenate biosynthetic process
GO:0046208 spermine catabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1yy5, PDBe:1yy5, PDBj:1yy5
PDBsum1yy5
PubMed15843025
UniProtP50264|FMS1_YEAST Polyamine oxidase FMS1 (Gene Name=FMS1)

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